So I tried F-Zero GX on the newest commit & it stays at around 30 fps.... but the '2 commits before' one gets 60 fps. Seems like a massive difference.
I've tried changing configurations to no avail, but once I re-installed the older commit I got 60 FPS again.

I hope my noticing this leads to an improvement in performance!

F-Zero GX typically would never play well for me unless I over-clocked it to 400% CPU emulation, now I do not have to do that, it "just works" at 60 fps!
I am using Vulkan, on a Nvidia GT 1030, nonfree drivers - Arch Linux derivative. 3.5GHz 6-core AMD FX-6300, 16GB DDR3 RAM @ 1600MHz.

It was a workaround for AMD drivers only - it shouldn't affect /anything/ on an nvidia system.

Looking at the commit I can't see anything wrong - maybe that was a bad bisect? Or you've got some unexpected settings that are getting picked up by some copies? Or there's another system issue at work (some throttling, load from another process etc.)